data_3AGO # _entry.id 3AGO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.398 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3AGO pdb_00003ago 10.2210/pdb3ago/pdb RCSB RCSB029230 ? ? WWPDB D_1000029230 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2010-07-07 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2012-04-04 4 'Structure model' 1 3 2023-11-01 5 'Structure model' 1 4 2024-10-30 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Refinement description' 7 5 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_initial_refinement_model 5 4 'Structure model' pdbx_struct_conn_angle 6 4 'Structure model' struct_conn 7 4 'Structure model' struct_site 8 5 'Structure model' pdbx_entry_details 9 5 'Structure model' pdbx_modification_feature # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_alt_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 18 4 'Structure model' '_pdbx_struct_conn_angle.value' 19 4 'Structure model' '_struct_conn.pdbx_dist_value' 20 4 'Structure model' '_struct_conn.pdbx_ptnr1_label_alt_id' 21 4 'Structure model' '_struct_conn.pdbx_ptnr2_label_alt_id' 22 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 23 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 24 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 25 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 26 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 27 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 28 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 29 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 30 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 31 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 32 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 33 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 34 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 35 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 3AGO _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2010-04-03 _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3AGN ;Ribonuclease U2 complexed with 3'-AMP ; unspecified PDB 1RTU 'Ribonuclease U2, Asp45 of which is isomerized to isoaspartate' unspecified # _audit_author.name 'Noguchi, S.' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title ;Isomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3'-monophosphate ; _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 66 _citation.page_first 843 _citation.page_last 849 _citation.year 2010 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20606265 _citation.pdbx_database_id_DOI 10.1107/S0907444910019621 # _citation_author.citation_id primary _citation_author.name 'Noguchi, S.' _citation_author.ordinal 1 _citation_author.identifier_ORCID ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer nat 'Ribonuclease U2' 12392.090 1 3.1.27.4 ? ? ? 2 non-polymer syn '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate' 347.221 1 ? ? ? ? 3 non-polymer syn 'CALCIUM ION' 40.078 2 ? ? ? ? 4 non-polymer syn 'CHLORIDE ION' 35.453 1 ? ? ? ? 5 water nat water 18.015 99 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'RNase U2' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;CDIPQSTNCGGNVYSNDDINTAIQGALDDVANGDRPDNYPHQYYDEASEDITLCCGSGPWSEFPLVYNGPYYSSRDNYVS PGPDRVIYQTNTGEFCATVTHTGAASYDGFTQCS ; _entity_poly.pdbx_seq_one_letter_code_can ;CDIPQSTNCGGNVYSNDDINTAIQGALDDVANGDRPDNYPHQYYDEASEDITLCCGSGPWSEFPLVYNGPYYSSRDNYVS PGPDRVIYQTNTGEFCATVTHTGAASYDGFTQCS ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate' 3AM 3 'CALCIUM ION' CA 4 'CHLORIDE ION' CL 5 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 CYS n 1 2 ASP n 1 3 ILE n 1 4 PRO n 1 5 GLN n 1 6 SER n 1 7 THR n 1 8 ASN n 1 9 CYS n 1 10 GLY n 1 11 GLY n 1 12 ASN n 1 13 VAL n 1 14 TYR n 1 15 SER n 1 16 ASN n 1 17 ASP n 1 18 ASP n 1 19 ILE n 1 20 ASN n 1 21 THR n 1 22 ALA n 1 23 ILE n 1 24 GLN n 1 25 GLY n 1 26 ALA n 1 27 LEU n 1 28 ASP n 1 29 ASP n 1 30 VAL n 1 31 ALA n 1 32 ASN n 1 33 GLY n 1 34 ASP n 1 35 ARG n 1 36 PRO n 1 37 ASP n 1 38 ASN n 1 39 TYR n 1 40 PRO n 1 41 HIS n 1 42 GLN n 1 43 TYR n 1 44 TYR n 1 45 ASP n 1 46 GLU n 1 47 ALA n 1 48 SER n 1 49 GLU n 1 50 ASP n 1 51 ILE n 1 52 THR n 1 53 LEU n 1 54 CYS n 1 55 CYS n 1 56 GLY n 1 57 SER n 1 58 GLY n 1 59 PRO n 1 60 TRP n 1 61 SER n 1 62 GLU n 1 63 PHE n 1 64 PRO n 1 65 LEU n 1 66 VAL n 1 67 TYR n 1 68 ASN n 1 69 GLY n 1 70 PRO n 1 71 TYR n 1 72 TYR n 1 73 SER n 1 74 SER n 1 75 ARG n 1 76 ASP n 1 77 ASN n 1 78 TYR n 1 79 VAL n 1 80 SER n 1 81 PRO n 1 82 GLY n 1 83 PRO n 1 84 ASP n 1 85 ARG n 1 86 VAL n 1 87 ILE n 1 88 TYR n 1 89 GLN n 1 90 THR n 1 91 ASN n 1 92 THR n 1 93 GLY n 1 94 GLU n 1 95 PHE n 1 96 CYS n 1 97 ALA n 1 98 THR n 1 99 VAL n 1 100 THR n 1 101 HIS n 1 102 THR n 1 103 GLY n 1 104 ALA n 1 105 ALA n 1 106 SER n 1 107 TYR n 1 108 ASP n 1 109 GLY n 1 110 PHE n 1 111 THR n 1 112 GLN n 1 113 CYS n 1 114 SER n # _entity_src_nat.entity_id 1 _entity_src_nat.pdbx_src_id 1 _entity_src_nat.pdbx_alt_source_flag sample _entity_src_nat.pdbx_beg_seq_num ? _entity_src_nat.pdbx_end_seq_num ? _entity_src_nat.common_name 'Smut fungus' _entity_src_nat.pdbx_organism_scientific 'Ustilago sphaerogena' _entity_src_nat.pdbx_ncbi_taxonomy_id 5271 _entity_src_nat.genus ? _entity_src_nat.species ? _entity_src_nat.strain ? _entity_src_nat.tissue ? _entity_src_nat.tissue_fraction ? _entity_src_nat.pdbx_secretion ? _entity_src_nat.pdbx_fragment ? _entity_src_nat.pdbx_variant ? _entity_src_nat.pdbx_cell_line ? _entity_src_nat.pdbx_atcc ? _entity_src_nat.pdbx_cellular_location ? _entity_src_nat.pdbx_organ ? _entity_src_nat.pdbx_organelle ? _entity_src_nat.pdbx_cell ? _entity_src_nat.pdbx_plasmid_name ? _entity_src_nat.pdbx_plasmid_details ? _entity_src_nat.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight 3AM non-polymer . '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate' "3'-AMP" 'C10 H14 N5 O7 P' 347.221 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 CYS 1 1 1 CYS CYS A . n A 1 2 ASP 2 2 2 ASP ASP A . n A 1 3 ILE 3 3 3 ILE ILE A . n A 1 4 PRO 4 4 4 PRO PRO A . n A 1 5 GLN 5 5 5 GLN GLN A . n A 1 6 SER 6 6 6 SER SER A . n A 1 7 THR 7 7 7 THR THR A . n A 1 8 ASN 8 8 8 ASN ASN A . n A 1 9 CYS 9 9 9 CYS CYS A . n A 1 10 GLY 10 10 10 GLY GLY A . n A 1 11 GLY 11 11 11 GLY GLY A . n A 1 12 ASN 12 12 12 ASN ASN A . n A 1 13 VAL 13 13 13 VAL VAL A . n A 1 14 TYR 14 14 14 TYR TYR A . n A 1 15 SER 15 15 15 SER SER A . n A 1 16 ASN 16 16 16 ASN ASN A . n A 1 17 ASP 17 17 17 ASP ASP A . n A 1 18 ASP 18 18 18 ASP ASP A . n A 1 19 ILE 19 19 19 ILE ILE A . n A 1 20 ASN 20 20 20 ASN ASN A . n A 1 21 THR 21 21 21 THR THR A . n A 1 22 ALA 22 22 22 ALA ALA A . n A 1 23 ILE 23 23 23 ILE ILE A . n A 1 24 GLN 24 24 24 GLN GLN A . n A 1 25 GLY 25 25 25 GLY GLY A . n A 1 26 ALA 26 26 26 ALA ALA A . n A 1 27 LEU 27 27 27 LEU LEU A . n A 1 28 ASP 28 28 28 ASP ASP A . n A 1 29 ASP 29 29 29 ASP ASP A . n A 1 30 VAL 30 30 30 VAL VAL A . n A 1 31 ALA 31 31 31 ALA ALA A . n A 1 32 ASN 32 32 32 ASN ASN A . n A 1 33 GLY 33 33 33 GLY GLY A . n A 1 34 ASP 34 34 34 ASP ASP A . n A 1 35 ARG 35 35 35 ARG ARG A . n A 1 36 PRO 36 36 36 PRO PRO A . n A 1 37 ASP 37 37 37 ASP ASP A . n A 1 38 ASN 38 38 38 ASN ASN A . n A 1 39 TYR 39 39 39 TYR TYR A . n A 1 40 PRO 40 40 40 PRO PRO A . n A 1 41 HIS 41 41 41 HIS HIS A . n A 1 42 GLN 42 42 42 GLN GLN A . n A 1 43 TYR 43 43 43 TYR TYR A . n A 1 44 TYR 44 44 44 TYR TYR A . n A 1 45 ASP 45 45 45 ASP ASP A . n A 1 46 GLU 46 46 46 GLU GLU A . n A 1 47 ALA 47 47 47 ALA ALA A . n A 1 48 SER 48 48 48 SER SER A . n A 1 49 GLU 49 49 49 GLU GLU A . n A 1 50 ASP 50 50 50 ASP ASP A . n A 1 51 ILE 51 51 51 ILE ILE A . n A 1 52 THR 52 52 52 THR THR A . n A 1 53 LEU 53 53 53 LEU LEU A . n A 1 54 CYS 54 54 54 CYS CYS A . n A 1 55 CYS 55 55 55 CYS CYS A . n A 1 56 GLY 56 56 56 GLY GLY A . n A 1 57 SER 57 57 57 SER SER A . n A 1 58 GLY 58 58 58 GLY GLY A . n A 1 59 PRO 59 59 59 PRO PRO A . n A 1 60 TRP 60 60 60 TRP TRP A . n A 1 61 SER 61 61 61 SER SER A . n A 1 62 GLU 62 62 62 GLU GLU A . n A 1 63 PHE 63 63 63 PHE PHE A . n A 1 64 PRO 64 64 64 PRO PRO A . n A 1 65 LEU 65 65 65 LEU LEU A . n A 1 66 VAL 66 66 66 VAL VAL A . n A 1 67 TYR 67 67 67 TYR TYR A . n A 1 68 ASN 68 68 68 ASN ASN A . n A 1 69 GLY 69 69 69 GLY GLY A . n A 1 70 PRO 70 70 70 PRO PRO A . n A 1 71 TYR 71 71 71 TYR TYR A . n A 1 72 TYR 72 72 72 TYR TYR A . n A 1 73 SER 73 73 73 SER SER A . n A 1 74 SER 74 74 74 SER SER A . n A 1 75 ARG 75 75 75 ARG ARG A . n A 1 76 ASP 76 76 76 ASP ASP A . n A 1 77 ASN 77 77 77 ASN ASN A . n A 1 78 TYR 78 78 78 TYR TYR A . n A 1 79 VAL 79 79 79 VAL VAL A . n A 1 80 SER 80 80 80 SER SER A . n A 1 81 PRO 81 81 81 PRO PRO A . n A 1 82 GLY 82 82 82 GLY GLY A . n A 1 83 PRO 83 83 83 PRO PRO A . n A 1 84 ASP 84 84 84 ASP ASP A . n A 1 85 ARG 85 85 85 ARG ARG A . n A 1 86 VAL 86 86 86 VAL VAL A . n A 1 87 ILE 87 87 87 ILE ILE A . n A 1 88 TYR 88 88 88 TYR TYR A . n A 1 89 GLN 89 89 89 GLN GLN A . n A 1 90 THR 90 90 90 THR THR A . n A 1 91 ASN 91 91 91 ASN ASN A . n A 1 92 THR 92 92 92 THR THR A . n A 1 93 GLY 93 93 93 GLY GLY A . n A 1 94 GLU 94 94 94 GLU GLU A . n A 1 95 PHE 95 95 95 PHE PHE A . n A 1 96 CYS 96 96 96 CYS CYS A . n A 1 97 ALA 97 97 97 ALA ALA A . n A 1 98 THR 98 98 98 THR THR A . n A 1 99 VAL 99 99 99 VAL VAL A . n A 1 100 THR 100 100 100 THR THR A . n A 1 101 HIS 101 101 101 HIS HIS A . n A 1 102 THR 102 102 102 THR THR A . n A 1 103 GLY 103 103 103 GLY GLY A . n A 1 104 ALA 104 104 104 ALA ALA A . n A 1 105 ALA 105 105 105 ALA ALA A . n A 1 106 SER 106 106 106 SER SER A . n A 1 107 TYR 107 107 107 TYR TYR A . n A 1 108 ASP 108 108 108 ASP ASP A . n A 1 109 GLY 109 109 109 GLY GLY A . n A 1 110 PHE 110 110 110 PHE PHE A . n A 1 111 THR 111 111 111 THR THR A . n A 1 112 GLN 112 112 112 GLN GLN A . n A 1 113 CYS 113 113 113 CYS CYS A . n A 1 114 SER 114 114 114 SER SER A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 3AM 1 115 115 3AM 3AM A . C 3 CA 1 116 116 CA CA A . D 3 CA 1 117 117 CA CA A . E 4 CL 1 118 118 CL CL A . F 5 HOH 1 119 119 HOH HOH A . F 5 HOH 2 120 120 HOH HOH A . F 5 HOH 3 121 121 HOH HOH A . F 5 HOH 4 122 122 HOH HOH A . F 5 HOH 5 123 123 HOH HOH A . F 5 HOH 6 124 124 HOH HOH A . F 5 HOH 7 125 125 HOH HOH A . F 5 HOH 8 126 126 HOH HOH A . F 5 HOH 9 127 127 HOH HOH A . F 5 HOH 10 128 128 HOH HOH A . F 5 HOH 11 129 129 HOH HOH A . F 5 HOH 12 130 130 HOH HOH A . F 5 HOH 13 131 131 HOH HOH A . F 5 HOH 14 132 132 HOH HOH A . F 5 HOH 15 133 133 HOH HOH A . F 5 HOH 16 134 134 HOH HOH A . F 5 HOH 17 135 135 HOH HOH A . F 5 HOH 18 138 138 HOH HOH A . F 5 HOH 19 139 139 HOH HOH A . F 5 HOH 20 140 140 HOH HOH A . F 5 HOH 21 141 141 HOH HOH A . F 5 HOH 22 142 142 HOH HOH A . F 5 HOH 23 143 143 HOH HOH A . F 5 HOH 24 144 144 HOH HOH A . F 5 HOH 25 145 145 HOH HOH A . F 5 HOH 26 146 146 HOH HOH A . F 5 HOH 27 147 147 HOH HOH A . F 5 HOH 28 148 148 HOH HOH A . F 5 HOH 29 149 149 HOH HOH A . F 5 HOH 30 150 150 HOH HOH A . F 5 HOH 31 151 151 HOH HOH A . F 5 HOH 32 152 152 HOH HOH A . F 5 HOH 33 153 153 HOH HOH A . F 5 HOH 34 154 154 HOH HOH A . F 5 HOH 35 155 155 HOH HOH A . F 5 HOH 36 156 156 HOH HOH A . F 5 HOH 37 157 157 HOH HOH A . F 5 HOH 38 158 158 HOH HOH A . F 5 HOH 39 159 159 HOH HOH A . F 5 HOH 40 160 160 HOH HOH A . F 5 HOH 41 161 161 HOH HOH A . F 5 HOH 42 162 162 HOH HOH A . F 5 HOH 43 163 163 HOH HOH A . F 5 HOH 44 164 164 HOH HOH A . F 5 HOH 45 165 165 HOH HOH A . F 5 HOH 46 166 166 HOH HOH A . F 5 HOH 47 167 167 HOH HOH A . F 5 HOH 48 168 168 HOH HOH A . F 5 HOH 49 169 169 HOH HOH A . F 5 HOH 50 170 170 HOH HOH A . F 5 HOH 51 171 171 HOH HOH A . F 5 HOH 52 172 172 HOH HOH A . F 5 HOH 53 173 173 HOH HOH A . F 5 HOH 54 174 174 HOH HOH A . F 5 HOH 55 175 175 HOH HOH A . F 5 HOH 56 176 176 HOH HOH A . F 5 HOH 57 177 177 HOH HOH A . F 5 HOH 58 178 178 HOH HOH A . F 5 HOH 59 179 179 HOH HOH A . F 5 HOH 60 180 180 HOH HOH A . F 5 HOH 61 181 181 HOH HOH A . F 5 HOH 62 182 182 HOH HOH A . F 5 HOH 63 183 183 HOH HOH A . F 5 HOH 64 184 184 HOH HOH A . F 5 HOH 65 185 185 HOH HOH A . F 5 HOH 66 186 186 HOH HOH A . F 5 HOH 67 187 187 HOH HOH A . F 5 HOH 68 188 188 HOH HOH A . F 5 HOH 69 189 189 HOH HOH A . F 5 HOH 70 190 190 HOH HOH A . F 5 HOH 71 191 191 HOH HOH A . F 5 HOH 72 192 192 HOH HOH A . F 5 HOH 73 193 193 HOH HOH A . F 5 HOH 74 194 194 HOH HOH A . F 5 HOH 75 195 195 HOH HOH A . F 5 HOH 76 196 196 HOH HOH A . F 5 HOH 77 197 197 HOH HOH A . F 5 HOH 78 198 198 HOH HOH A . F 5 HOH 79 199 199 HOH HOH A . F 5 HOH 80 200 200 HOH HOH A . F 5 HOH 81 201 201 HOH HOH A . F 5 HOH 82 202 202 HOH HOH A . F 5 HOH 83 203 203 HOH HOH A . F 5 HOH 84 204 204 HOH HOH A . F 5 HOH 85 205 205 HOH HOH A . F 5 HOH 86 206 206 HOH HOH A . F 5 HOH 87 207 207 HOH HOH A . F 5 HOH 88 208 208 HOH HOH A . F 5 HOH 89 209 209 HOH HOH A . F 5 HOH 90 210 210 HOH HOH A . F 5 HOH 91 211 211 HOH HOH A . F 5 HOH 92 212 212 HOH HOH A . F 5 HOH 93 213 213 HOH HOH A . F 5 HOH 94 214 214 HOH HOH A . F 5 HOH 95 215 215 HOH HOH A . F 5 HOH 96 216 216 HOH HOH A . F 5 HOH 97 217 217 HOH HOH A . F 5 HOH 98 219 219 HOH HOH A . F 5 HOH 99 220 220 HOH HOH A . # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 REFMAC . ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 2 PDB_EXTRACT 3.100 'Jan. 22, 2010' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 3 HKL-2000 . ? ? ? ? 'data collection' ? ? ? 4 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 5 SCALEPACK . ? ? ? ? 'data scaling' ? ? ? 6 MOLREP . ? ? ? ? phasing ? ? ? # _cell.entry_id 3AGO _cell.length_a 34.586 _cell.length_b 39.425 _cell.length_c 31.646 _cell.angle_alpha 90.00 _cell.angle_beta 108.98 _cell.angle_gamma 90.00 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3AGO _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? # _exptl.crystals_number 1 _exptl.entry_id 3AGO _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.density_Matthews 1.6464 _exptl_crystal.density_diffrn ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_percent_sol 25.2916 _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.pH 3.75 _exptl_crystal_grow.temp 293 _exptl_crystal_grow.pdbx_details '12.5% PEG 8000, 200mM calcium acetate, 100mM sodium cacodylate, 240mM HCl, pH 3.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 95 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4r' _diffrn_detector.pdbx_collection_date 2010-01-01 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator 'TRIANGULAR Si(111)' _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.978 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-6A' _diffrn_source.pdbx_wavelength_list 0.978 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline BL-6A # _reflns.entry_id 3AGO _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I 0 _reflns.d_resolution_high 0.99 _reflns.d_resolution_low 34.3 _reflns.number_all ? _reflns.number_obs 43053 _reflns.percent_possible_obs 96.2 _reflns.pdbx_Rmerge_I_obs 0.061 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 58.0 _reflns.B_iso_Wilson_estimate 9.8 _reflns.pdbx_redundancy 9.2 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 0.99 _reflns_shell.d_res_low 1.02 _reflns_shell.percent_possible_obs ? _reflns_shell.percent_possible_all 92.4 _reflns_shell.Rmerge_I_obs 0.433 _reflns_shell.meanI_over_sigI_obs 6.6 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_redundancy 6.7 _reflns_shell.number_unique_all 3011 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3AGO _refine.ls_d_res_high 0.990 _refine.ls_d_res_low 32.710 _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 96.040 _refine.ls_number_reflns_obs 40857 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY' _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.151 _refine.ls_R_factor_R_work 0.150 _refine.ls_wR_factor_R_work 0.147 _refine.ls_R_factor_R_free 0.162 _refine.ls_wR_factor_R_free 0.160 _refine.ls_percent_reflns_R_free 5.100 _refine.ls_number_reflns_R_free 2196 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 9.168 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model anisotropic _refine.aniso_B[1][1] 0.520 _refine.aniso_B[2][2] -1.000 _refine.aniso_B[3][3] 0.580 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.140 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.975 _refine.correlation_coeff_Fo_to_Fc_free 0.976 _refine.overall_SU_R_Cruickshank_DPI 0.027 _refine.overall_SU_R_free 0.026 _refine.pdbx_overall_ESU_R 0.028 _refine.pdbx_overall_ESU_R_Free 0.026 _refine.overall_SU_ML 0.016 _refine.overall_SU_B 0.655 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.400 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model 'PDB ENTRY 1RTU' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.915 _refine.B_iso_max 40.26 _refine.B_iso_min 4.22 _refine.occupancy_max 1.00 _refine.occupancy_min 0.40 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_phase_error ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 3AGO _refine_analyze.Luzzati_coordinate_error_obs 0.028 _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free 0.026 _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 870 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 26 _refine_hist.number_atoms_solvent 99 _refine_hist.number_atoms_total 995 _refine_hist.d_res_high 0.990 _refine_hist.d_res_low 32.710 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 949 0.014 0.021 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 587 0.006 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1309 1.900 1.964 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 1437 3.524 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 116 7.373 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 51 36.358 25.294 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 119 11.827 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 4 17.894 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 134 0.091 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 1104 0.009 0.021 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 194 0.002 0.020 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 579 1.411 1.500 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 235 0.412 1.500 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 940 2.166 2.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 370 2.848 3.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 369 4.030 4.500 ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 1535 1.118 3.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 0.990 _refine_ls_shell.d_res_low 1.016 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 92.160 _refine_ls_shell.number_reflns_R_work 2849 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.382 _refine_ls_shell.R_factor_R_free 0.374 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 162 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 3011 _refine_ls_shell.number_reflns_obs 3011 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3AGO _struct.title ;Crystal Structure of Ustilago sphaerogena Ribonuclease U2 complexed with adenosine 3'-monophosphate ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3AGO _struct_keywords.text 'Purine-specific endo-ribonuclease, HYDROLASE' _struct_keywords.pdbx_keywords HYDROLASE # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 4 ? F N N 5 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code RNU2_USTSP _struct_ref.pdbx_db_accession P00654 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;CDIPQSTNCGGNVYSNDDINTAIQGALDDVANGDRPDNYPHQYYDEASEDITLCCGSGPWSEFPLVYNGPYYSSRDNYVS PGPDRVIYQTNTGEFCATVTHTGAASYDGFTQCS ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3AGO _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 114 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P00654 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 114 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 114 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 ASN A 16 ? ASP A 29 ? ASN A 16 ASP A 29 1 ? 14 HELX_P HELX_P2 2 GLU A 46 ? ASP A 50 ? GLU A 46 ASP A 50 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf ? ? A CYS 1 SG ? ? ? 1_555 A CYS 54 SG ? ? A CYS 1 A CYS 54 1_555 ? ? ? ? ? ? ? 2.011 ? ? disulf2 disulf ? ? A CYS 9 SG ? ? ? 1_555 A CYS 113 SG ? ? A CYS 9 A CYS 113 1_555 ? ? ? ? ? ? ? 2.041 ? ? disulf3 disulf ? ? A CYS 55 SG ? ? ? 1_555 A CYS 96 SG ? ? A CYS 55 A CYS 96 1_555 ? ? ? ? ? ? ? 2.031 ? ? metalc1 metalc ? ? A ASP 29 OD1 ? ? ? 1_555 C CA . CA B ? A ASP 29 A CA 116 1_555 ? ? ? ? ? ? ? 2.453 ? ? metalc2 metalc ? ? A ASP 29 OD1 ? ? ? 1_555 C CA . CA A ? A ASP 29 A CA 116 1_555 ? ? ? ? ? ? ? 2.578 ? ? metalc3 metalc ? ? A ALA 31 O ? ? ? 1_555 C CA . CA A ? A ALA 31 A CA 116 1_555 ? ? ? ? ? ? ? 2.336 ? ? metalc4 metalc ? ? A ALA 31 O ? ? ? 1_555 C CA . CA B ? A ALA 31 A CA 116 1_555 ? ? ? ? ? ? ? 2.534 ? ? metalc5 metalc ? ? A ASN 32 OD1 ? ? ? 1_555 C CA . CA B ? A ASN 32 A CA 116 1_555 ? ? ? ? ? ? ? 2.670 ? ? metalc6 metalc ? ? A TYR 39 O ? ? ? 1_555 C CA . CA A ? A TYR 39 A CA 116 1_555 ? ? ? ? ? ? ? 2.854 ? ? metalc7 metalc ? ? A ASP 45 OD1 ? ? ? 1_555 D CA . CA ? ? A ASP 45 A CA 117 1_555 ? ? ? ? ? ? ? 2.377 ? ? metalc8 metalc ? ? A ILE 51 O ? ? ? 1_555 D CA . CA ? ? A ILE 51 A CA 117 1_555 ? ? ? ? ? ? ? 2.301 ? ? metalc9 metalc ? ? C CA . CA A ? ? 1_555 F HOH . O ? ? A CA 116 A HOH 198 1_555 ? ? ? ? ? ? ? 3.182 ? ? metalc10 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? A CA 117 A HOH 141 1_555 ? ? ? ? ? ? ? 2.460 ? ? metalc11 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? A CA 117 A HOH 215 1_555 ? ? ? ? ? ? ? 2.388 ? ? metalc12 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? A CA 117 A HOH 216 1_555 ? ? ? ? ? ? ? 2.721 ? ? metalc13 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? A CA 117 A HOH 220 1_555 ? ? ? ? ? ? ? 2.631 ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? metalc ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OD1 ? A ASP 29 ? A ASP 29 ? 1_555 CA B C CA . ? A CA 116 ? 1_555 O ? A ALA 31 ? A ALA 31 ? 1_555 99.8 ? 2 OD1 ? A ASP 29 ? A ASP 29 ? 1_555 CA B C CA . ? A CA 116 ? 1_555 OD1 ? A ASN 32 ? A ASN 32 ? 1_555 91.8 ? 3 O ? A ALA 31 ? A ALA 31 ? 1_555 CA B C CA . ? A CA 116 ? 1_555 OD1 ? A ASN 32 ? A ASN 32 ? 1_555 77.1 ? 4 OD1 ? A ASP 29 ? A ASP 29 ? 1_555 CA A C CA . ? A CA 116 ? 1_555 O ? A ALA 31 ? A ALA 31 ? 1_555 101.8 ? 5 OD1 ? A ASP 29 ? A ASP 29 ? 1_555 CA A C CA . ? A CA 116 ? 1_555 O ? A TYR 39 ? A TYR 39 ? 1_555 104.7 ? 6 O ? A ALA 31 ? A ALA 31 ? 1_555 CA A C CA . ? A CA 116 ? 1_555 O ? A TYR 39 ? A TYR 39 ? 1_555 89.5 ? 7 OD1 ? A ASP 29 ? A ASP 29 ? 1_555 CA A C CA . ? A CA 116 ? 1_555 O ? F HOH . ? A HOH 198 ? 1_555 55.0 ? 8 O ? A ALA 31 ? A ALA 31 ? 1_555 CA A C CA . ? A CA 116 ? 1_555 O ? F HOH . ? A HOH 198 ? 1_555 79.3 ? 9 O ? A TYR 39 ? A TYR 39 ? 1_555 CA A C CA . ? A CA 116 ? 1_555 O ? F HOH . ? A HOH 198 ? 1_555 55.0 ? 10 OD1 ? A ASP 45 ? A ASP 45 ? 1_555 CA ? D CA . ? A CA 117 ? 1_555 O ? A ILE 51 ? A ILE 51 ? 1_555 113.5 ? 11 OD1 ? A ASP 45 ? A ASP 45 ? 1_555 CA ? D CA . ? A CA 117 ? 1_555 O ? F HOH . ? A HOH 141 ? 1_555 79.3 ? 12 O ? A ILE 51 ? A ILE 51 ? 1_555 CA ? D CA . ? A CA 117 ? 1_555 O ? F HOH . ? A HOH 141 ? 1_555 165.8 ? 13 OD1 ? A ASP 45 ? A ASP 45 ? 1_555 CA ? D CA . ? A CA 117 ? 1_555 O ? F HOH . ? A HOH 215 ? 1_555 152.6 ? 14 O ? A ILE 51 ? A ILE 51 ? 1_555 CA ? D CA . ? A CA 117 ? 1_555 O ? F HOH . ? A HOH 215 ? 1_555 80.7 ? 15 O ? F HOH . ? A HOH 141 ? 1_555 CA ? D CA . ? A CA 117 ? 1_555 O ? F HOH . ? A HOH 215 ? 1_555 85.2 ? 16 OD1 ? A ASP 45 ? A ASP 45 ? 1_555 CA ? D CA . ? A CA 117 ? 1_555 O ? F HOH . ? A HOH 216 ? 1_555 72.0 ? 17 O ? A ILE 51 ? A ILE 51 ? 1_555 CA ? D CA . ? A CA 117 ? 1_555 O ? F HOH . ? A HOH 216 ? 1_555 74.2 ? 18 O ? F HOH . ? A HOH 141 ? 1_555 CA ? D CA . ? A CA 117 ? 1_555 O ? F HOH . ? A HOH 216 ? 1_555 117.2 ? 19 O ? F HOH . ? A HOH 215 ? 1_555 CA ? D CA . ? A CA 117 ? 1_555 O ? F HOH . ? A HOH 216 ? 1_555 135.4 ? 20 OD1 ? A ASP 45 ? A ASP 45 ? 1_555 CA ? D CA . ? A CA 117 ? 1_555 O ? F HOH . ? A HOH 220 ? 1_555 78.4 ? 21 O ? A ILE 51 ? A ILE 51 ? 1_555 CA ? D CA . ? A CA 117 ? 1_555 O ? F HOH . ? A HOH 220 ? 1_555 82.4 ? 22 O ? F HOH . ? A HOH 141 ? 1_555 CA ? D CA . ? A CA 117 ? 1_555 O ? F HOH . ? A HOH 220 ? 1_555 94.8 ? 23 O ? F HOH . ? A HOH 215 ? 1_555 CA ? D CA . ? A CA 117 ? 1_555 O ? F HOH . ? A HOH 220 ? 1_555 80.6 ? 24 O ? F HOH . ? A HOH 216 ? 1_555 CA ? D CA . ? A CA 117 ? 1_555 O ? F HOH . ? A HOH 220 ? 1_555 130.2 ? # loop_ _pdbx_modification_feature.ordinal _pdbx_modification_feature.label_comp_id _pdbx_modification_feature.label_asym_id _pdbx_modification_feature.label_seq_id _pdbx_modification_feature.label_alt_id _pdbx_modification_feature.modified_residue_label_comp_id _pdbx_modification_feature.modified_residue_label_asym_id _pdbx_modification_feature.modified_residue_label_seq_id _pdbx_modification_feature.modified_residue_label_alt_id _pdbx_modification_feature.auth_comp_id _pdbx_modification_feature.auth_asym_id _pdbx_modification_feature.auth_seq_id _pdbx_modification_feature.PDB_ins_code _pdbx_modification_feature.symmetry _pdbx_modification_feature.modified_residue_auth_comp_id _pdbx_modification_feature.modified_residue_auth_asym_id _pdbx_modification_feature.modified_residue_auth_seq_id _pdbx_modification_feature.modified_residue_PDB_ins_code _pdbx_modification_feature.modified_residue_symmetry _pdbx_modification_feature.comp_id_linking_atom _pdbx_modification_feature.modified_residue_id_linking_atom _pdbx_modification_feature.modified_residue_id _pdbx_modification_feature.ref_pcm_id _pdbx_modification_feature.ref_comp_id _pdbx_modification_feature.type _pdbx_modification_feature.category 1 CYS A 1 ? CYS A 54 ? CYS A 1 ? 1_555 CYS A 54 ? 1_555 SG SG . . . None 'Disulfide bridge' 2 CYS A 9 ? CYS A 113 ? CYS A 9 ? 1_555 CYS A 113 ? 1_555 SG SG . . . None 'Disulfide bridge' 3 CYS A 55 ? CYS A 96 ? CYS A 55 ? 1_555 CYS A 96 ? 1_555 SG SG . . . None 'Disulfide bridge' # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 TYR 39 A . ? TYR 39 A PRO 40 A ? PRO 40 A 1 -3.75 2 GLY 58 A . ? GLY 58 A PRO 59 A ? PRO 59 A 1 7.25 3 GLY 69 A . ? GLY 69 A PRO 70 A ? PRO 70 A 1 6.15 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 2 ? B ? 5 ? C ? 2 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel B 4 5 ? anti-parallel C 1 2 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 SER A 6 ? CYS A 9 ? SER A 6 CYS A 9 A 2 ASN A 12 ? SER A 15 ? ASN A 12 SER A 15 B 1 HIS A 41 ? TYR A 43 ? HIS A 41 TYR A 43 B 2 TRP A 60 ? PRO A 64 ? TRP A 60 PRO A 64 B 3 ASP A 84 ? GLN A 89 ? ASP A 84 GLN A 89 B 4 PHE A 95 ? THR A 100 ? PHE A 95 THR A 100 B 5 THR A 111 ? GLN A 112 ? THR A 111 GLN A 112 C 1 SER A 73 ? SER A 74 ? SER A 73 SER A 74 C 2 ASN A 77 ? TYR A 78 ? ASN A 77 TYR A 78 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N CYS A 9 ? N CYS A 9 O ASN A 12 ? O ASN A 12 B 1 2 N HIS A 41 ? N HIS A 41 O GLU A 62 ? O GLU A 62 B 2 3 N SER A 61 ? N SER A 61 O TYR A 88 ? O TYR A 88 B 3 4 N ARG A 85 ? N ARG A 85 O VAL A 99 ? O VAL A 99 B 4 5 N THR A 100 ? N THR A 100 O THR A 111 ? O THR A 111 C 1 2 N SER A 74 ? N SER A 74 O ASN A 77 ? O ASN A 77 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A 3AM 115 ? 16 'BINDING SITE FOR RESIDUE 3AM A 115' AC2 Software A CA 116 ? 5 'BINDING SITE FOR RESIDUE CA A 116' AC3 Software A CA 117 ? 6 'BINDING SITE FOR RESIDUE CA A 117' AC4 Software A CL 118 ? 5 'BINDING SITE FOR RESIDUE CL A 118' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 16 TYR A 39 ? TYR A 39 . ? 1_555 ? 2 AC1 16 HIS A 41 ? HIS A 41 . ? 1_555 ? 3 AC1 16 GLN A 42 ? GLN A 42 . ? 1_555 ? 4 AC1 16 TYR A 43 ? TYR A 43 . ? 1_555 ? 5 AC1 16 TYR A 44 ? TYR A 44 . ? 1_555 ? 6 AC1 16 GLU A 46 ? GLU A 46 . ? 1_555 ? 7 AC1 16 GLU A 49 ? GLU A 49 . ? 1_555 ? 8 AC1 16 GLU A 62 ? GLU A 62 . ? 1_555 ? 9 AC1 16 ARG A 85 ? ARG A 85 . ? 1_555 ? 10 AC1 16 HIS A 101 ? HIS A 101 . ? 1_555 ? 11 AC1 16 ASP A 108 ? ASP A 108 . ? 1_555 ? 12 AC1 16 PHE A 110 ? PHE A 110 . ? 1_555 ? 13 AC1 16 HOH F . ? HOH A 149 . ? 1_555 ? 14 AC1 16 HOH F . ? HOH A 159 . ? 1_555 ? 15 AC1 16 HOH F . ? HOH A 162 . ? 1_555 ? 16 AC1 16 HOH F . ? HOH A 189 . ? 1_555 ? 17 AC2 5 ASP A 29 ? ASP A 29 . ? 1_555 ? 18 AC2 5 ALA A 31 ? ALA A 31 . ? 1_555 ? 19 AC2 5 ASN A 32 ? ASN A 32 . ? 1_555 ? 20 AC2 5 ASN A 38 ? ASN A 38 . ? 1_555 ? 21 AC2 5 TYR A 39 ? TYR A 39 . ? 1_555 ? 22 AC3 6 ASP A 45 ? ASP A 45 . ? 1_555 ? 23 AC3 6 ILE A 51 ? ILE A 51 . ? 1_555 ? 24 AC3 6 HOH F . ? HOH A 141 . ? 1_555 ? 25 AC3 6 HOH F . ? HOH A 215 . ? 1_555 ? 26 AC3 6 HOH F . ? HOH A 216 . ? 1_555 ? 27 AC3 6 HOH F . ? HOH A 220 . ? 1_555 ? 28 AC4 5 ARG A 35 ? ARG A 35 . ? 1_555 ? 29 AC4 5 ASN A 38 ? ASN A 38 . ? 1_555 ? 30 AC4 5 TYR A 39 ? TYR A 39 . ? 1_555 ? 31 AC4 5 TYR A 71 ? TYR A 71 . ? 1_555 ? 32 AC4 5 SER A 73 ? SER A 73 . ? 1_555 ? # _pdbx_entry_details.entry_id 3AGO _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? _pdbx_entry_details.has_protein_modification Y # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ASP A 34 ? ? -93.64 32.47 2 1 ASP A 37 ? ? -110.88 76.47 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal 3AM O1P O N N 1 3AM P P N N 2 3AM O2P O N N 3 3AM O3P O N N 4 3AM "O2'" O N N 5 3AM "C2'" C N R 6 3AM "C3'" C N S 7 3AM "O3'" O N N 8 3AM "C1'" C N R 9 3AM "O4'" O N N 10 3AM "C4'" C N R 11 3AM "C5'" C N N 12 3AM "O5'" O N N 13 3AM N9 N Y N 14 3AM C8 C Y N 15 3AM N7 N Y N 16 3AM C5 C Y N 17 3AM C6 C Y N 18 3AM N6 N N N 19 3AM C4 C Y N 20 3AM N3 N Y N 21 3AM C2 C Y N 22 3AM N1 N Y N 23 3AM HO2P H N N 24 3AM HO3P H N N 25 3AM "HO2'" H N N 26 3AM "H2'" H N N 27 3AM "H3'" H N N 28 3AM "H1'" H N N 29 3AM "H4'" H N N 30 3AM "H5'" H N N 31 3AM "H5'A" H N N 32 3AM "HO5'" H N N 33 3AM H8 H N N 34 3AM HN6 H N N 35 3AM HN6A H N N 36 3AM H2 H N N 37 ALA N N N N 38 ALA CA C N S 39 ALA C C N N 40 ALA O O N N 41 ALA CB C N N 42 ALA OXT O N N 43 ALA H H N N 44 ALA H2 H N N 45 ALA HA H N N 46 ALA HB1 H N N 47 ALA HB2 H N N 48 ALA HB3 H N N 49 ALA HXT H N N 50 ARG N N N N 51 ARG CA C N S 52 ARG C C N N 53 ARG O O N N 54 ARG CB C N N 55 ARG CG C N N 56 ARG CD C N N 57 ARG NE N N N 58 ARG CZ C N N 59 ARG NH1 N N N 60 ARG NH2 N N N 61 ARG OXT O N N 62 ARG H H N N 63 ARG H2 H N N 64 ARG HA H N N 65 ARG HB2 H N N 66 ARG HB3 H N N 67 ARG HG2 H N N 68 ARG HG3 H N N 69 ARG HD2 H N N 70 ARG HD3 H N N 71 ARG HE H N N 72 ARG HH11 H N N 73 ARG HH12 H N N 74 ARG HH21 H N N 75 ARG HH22 H N N 76 ARG HXT H N N 77 ASN N N N N 78 ASN CA C N S 79 ASN C C N N 80 ASN O O N N 81 ASN CB C N N 82 ASN CG C N N 83 ASN OD1 O N N 84 ASN ND2 N N N 85 ASN OXT O N N 86 ASN H H N N 87 ASN H2 H N N 88 ASN HA H N N 89 ASN HB2 H N N 90 ASN HB3 H N N 91 ASN HD21 H N N 92 ASN HD22 H N N 93 ASN HXT H N N 94 ASP N N N N 95 ASP CA C N S 96 ASP C C N N 97 ASP O O N N 98 ASP CB C N N 99 ASP CG C N N 100 ASP OD1 O N N 101 ASP OD2 O N N 102 ASP OXT O N N 103 ASP H H N N 104 ASP H2 H N N 105 ASP HA H N N 106 ASP HB2 H N N 107 ASP HB3 H N N 108 ASP HD2 H N N 109 ASP HXT H N N 110 CA CA CA N N 111 CL CL CL N N 112 CYS N N N N 113 CYS CA C N R 114 CYS C C N N 115 CYS O O N N 116 CYS CB C N N 117 CYS SG S N N 118 CYS OXT O N N 119 CYS H H N N 120 CYS H2 H N N 121 CYS HA H N N 122 CYS HB2 H N N 123 CYS HB3 H N N 124 CYS HG H N N 125 CYS HXT H N N 126 GLN N N N N 127 GLN CA C N S 128 GLN C C N N 129 GLN O O N N 130 GLN CB C N N 131 GLN CG C N N 132 GLN CD C N N 133 GLN OE1 O N N 134 GLN NE2 N N N 135 GLN OXT O N N 136 GLN H H N N 137 GLN H2 H N N 138 GLN HA H N N 139 GLN HB2 H N N 140 GLN HB3 H N N 141 GLN HG2 H N N 142 GLN HG3 H N N 143 GLN HE21 H N N 144 GLN HE22 H N N 145 GLN HXT H N N 146 GLU N N N N 147 GLU CA C N S 148 GLU C C N N 149 GLU O O N N 150 GLU CB C N N 151 GLU CG C N N 152 GLU CD C N N 153 GLU OE1 O N N 154 GLU OE2 O N N 155 GLU OXT O N N 156 GLU H H N N 157 GLU H2 H N N 158 GLU HA H N N 159 GLU HB2 H N N 160 GLU HB3 H N N 161 GLU HG2 H N N 162 GLU HG3 H N N 163 GLU HE2 H N N 164 GLU HXT H N N 165 GLY N N N N 166 GLY CA C N N 167 GLY C C N N 168 GLY O O N N 169 GLY OXT O N N 170 GLY H H N N 171 GLY H2 H N N 172 GLY HA2 H N N 173 GLY HA3 H N N 174 GLY HXT H N N 175 HIS N N N N 176 HIS CA C N S 177 HIS C C N N 178 HIS O O N N 179 HIS CB C N N 180 HIS CG C Y N 181 HIS ND1 N Y N 182 HIS CD2 C Y N 183 HIS CE1 C Y N 184 HIS NE2 N Y N 185 HIS OXT O N N 186 HIS H H N N 187 HIS H2 H N N 188 HIS HA H N N 189 HIS HB2 H N N 190 HIS HB3 H N N 191 HIS HD1 H N N 192 HIS HD2 H N N 193 HIS HE1 H N N 194 HIS HE2 H N N 195 HIS HXT H N N 196 HOH O O N N 197 HOH H1 H N N 198 HOH H2 H N N 199 ILE N N N N 200 ILE CA C N S 201 ILE C C N N 202 ILE O O N N 203 ILE CB C N S 204 ILE CG1 C N N 205 ILE CG2 C N N 206 ILE CD1 C N N 207 ILE OXT O N N 208 ILE H H N N 209 ILE H2 H N N 210 ILE HA H N N 211 ILE HB H N N 212 ILE HG12 H N N 213 ILE HG13 H N N 214 ILE HG21 H N N 215 ILE HG22 H N N 216 ILE HG23 H N N 217 ILE HD11 H N N 218 ILE HD12 H N N 219 ILE HD13 H N N 220 ILE HXT H N N 221 LEU N N N N 222 LEU CA C N S 223 LEU C C N N 224 LEU O O N N 225 LEU CB C N N 226 LEU CG C N N 227 LEU CD1 C N N 228 LEU CD2 C N N 229 LEU OXT O N N 230 LEU H H N N 231 LEU H2 H N N 232 LEU HA H N N 233 LEU HB2 H N N 234 LEU HB3 H N N 235 LEU HG H N N 236 LEU HD11 H N N 237 LEU HD12 H N N 238 LEU HD13 H N N 239 LEU HD21 H N N 240 LEU HD22 H N N 241 LEU HD23 H N N 242 LEU HXT H N N 243 PHE N N N N 244 PHE CA C N S 245 PHE C C N N 246 PHE O O N N 247 PHE CB C N N 248 PHE CG C Y N 249 PHE CD1 C Y N 250 PHE CD2 C Y N 251 PHE CE1 C Y N 252 PHE CE2 C Y N 253 PHE CZ C Y N 254 PHE OXT O N N 255 PHE H H N N 256 PHE H2 H N N 257 PHE HA H N N 258 PHE HB2 H N N 259 PHE HB3 H N N 260 PHE HD1 H N N 261 PHE HD2 H N N 262 PHE HE1 H N N 263 PHE HE2 H N N 264 PHE HZ H N N 265 PHE HXT H N N 266 PRO N N N N 267 PRO CA C N S 268 PRO C C N N 269 PRO O O N N 270 PRO CB C N N 271 PRO CG C N N 272 PRO CD C N N 273 PRO OXT O N N 274 PRO H H N N 275 PRO HA H N N 276 PRO HB2 H N N 277 PRO HB3 H N N 278 PRO HG2 H N N 279 PRO HG3 H N N 280 PRO HD2 H N N 281 PRO HD3 H N N 282 PRO HXT H N N 283 SER N N N N 284 SER CA C N S 285 SER C C N N 286 SER O O N N 287 SER CB C N N 288 SER OG O N N 289 SER OXT O N N 290 SER H H N N 291 SER H2 H N N 292 SER HA H N N 293 SER HB2 H N N 294 SER HB3 H N N 295 SER HG H N N 296 SER HXT H N N 297 THR N N N N 298 THR CA C N S 299 THR C C N N 300 THR O O N N 301 THR CB C N R 302 THR OG1 O N N 303 THR CG2 C N N 304 THR OXT O N N 305 THR H H N N 306 THR H2 H N N 307 THR HA H N N 308 THR HB H N N 309 THR HG1 H N N 310 THR HG21 H N N 311 THR HG22 H N N 312 THR HG23 H N N 313 THR HXT H N N 314 TRP N N N N 315 TRP CA C N S 316 TRP C C N N 317 TRP O O N N 318 TRP CB C N N 319 TRP CG C Y N 320 TRP CD1 C Y N 321 TRP CD2 C Y N 322 TRP NE1 N Y N 323 TRP CE2 C Y N 324 TRP CE3 C Y N 325 TRP CZ2 C Y N 326 TRP CZ3 C Y N 327 TRP CH2 C Y N 328 TRP OXT O N N 329 TRP H H N N 330 TRP H2 H N N 331 TRP HA H N N 332 TRP HB2 H N N 333 TRP HB3 H N N 334 TRP HD1 H N N 335 TRP HE1 H N N 336 TRP HE3 H N N 337 TRP HZ2 H N N 338 TRP HZ3 H N N 339 TRP HH2 H N N 340 TRP HXT H N N 341 TYR N N N N 342 TYR CA C N S 343 TYR C C N N 344 TYR O O N N 345 TYR CB C N N 346 TYR CG C Y N 347 TYR CD1 C Y N 348 TYR CD2 C Y N 349 TYR CE1 C Y N 350 TYR CE2 C Y N 351 TYR CZ C Y N 352 TYR OH O N N 353 TYR OXT O N N 354 TYR H H N N 355 TYR H2 H N N 356 TYR HA H N N 357 TYR HB2 H N N 358 TYR HB3 H N N 359 TYR HD1 H N N 360 TYR HD2 H N N 361 TYR HE1 H N N 362 TYR HE2 H N N 363 TYR HH H N N 364 TYR HXT H N N 365 VAL N N N N 366 VAL CA C N S 367 VAL C C N N 368 VAL O O N N 369 VAL CB C N N 370 VAL CG1 C N N 371 VAL CG2 C N N 372 VAL OXT O N N 373 VAL H H N N 374 VAL H2 H N N 375 VAL HA H N N 376 VAL HB H N N 377 VAL HG11 H N N 378 VAL HG12 H N N 379 VAL HG13 H N N 380 VAL HG21 H N N 381 VAL HG22 H N N 382 VAL HG23 H N N 383 VAL HXT H N N 384 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 3AM O1P P doub N N 1 3AM P O2P sing N N 2 3AM P O3P sing N N 3 3AM P "O3'" sing N N 4 3AM "O2'" "C2'" sing N N 5 3AM "C2'" "C3'" sing N N 6 3AM "C2'" "C1'" sing N N 7 3AM "C3'" "O3'" sing N N 8 3AM "C3'" "C4'" sing N N 9 3AM "C1'" "O4'" sing N N 10 3AM "C1'" N9 sing N N 11 3AM "O4'" "C4'" sing N N 12 3AM "C4'" "C5'" sing N N 13 3AM "C5'" "O5'" sing N N 14 3AM N9 C8 sing Y N 15 3AM N9 C4 sing Y N 16 3AM C8 N7 doub Y N 17 3AM N7 C5 sing Y N 18 3AM C5 C6 doub Y N 19 3AM C5 C4 sing Y N 20 3AM C6 N6 sing N N 21 3AM C6 N1 sing Y N 22 3AM C4 N3 doub Y N 23 3AM N3 C2 sing Y N 24 3AM C2 N1 doub Y N 25 3AM O2P HO2P sing N N 26 3AM O3P HO3P sing N N 27 3AM "O2'" "HO2'" sing N N 28 3AM "C2'" "H2'" sing N N 29 3AM "C3'" "H3'" sing N N 30 3AM "C1'" "H1'" sing N N 31 3AM "C4'" "H4'" sing N N 32 3AM "C5'" "H5'" sing N N 33 3AM "C5'" "H5'A" sing N N 34 3AM "O5'" "HO5'" sing N N 35 3AM C8 H8 sing N N 36 3AM N6 HN6 sing N N 37 3AM N6 HN6A sing N N 38 3AM C2 H2 sing N N 39 ALA N CA sing N N 40 ALA N H sing N N 41 ALA N H2 sing N N 42 ALA CA C sing N N 43 ALA CA CB sing N N 44 ALA CA HA sing N N 45 ALA C O doub N N 46 ALA C OXT sing N N 47 ALA CB HB1 sing N N 48 ALA CB HB2 sing N N 49 ALA CB HB3 sing N N 50 ALA OXT HXT sing N N 51 ARG N CA sing N N 52 ARG N H sing N N 53 ARG N H2 sing N N 54 ARG CA C sing N N 55 ARG CA CB sing N N 56 ARG CA HA sing N N 57 ARG C O doub N N 58 ARG C OXT sing N N 59 ARG CB CG sing N N 60 ARG CB HB2 sing N N 61 ARG CB HB3 sing N N 62 ARG CG CD sing N N 63 ARG CG HG2 sing N N 64 ARG CG HG3 sing N N 65 ARG CD NE sing N N 66 ARG CD HD2 sing N N 67 ARG CD HD3 sing N N 68 ARG NE CZ sing N N 69 ARG NE HE sing N N 70 ARG CZ NH1 sing N N 71 ARG CZ NH2 doub N N 72 ARG NH1 HH11 sing N N 73 ARG NH1 HH12 sing N N 74 ARG NH2 HH21 sing N N 75 ARG NH2 HH22 sing N N 76 ARG OXT HXT sing N N 77 ASN N CA sing N N 78 ASN N H sing N N 79 ASN N H2 sing N N 80 ASN CA C sing N N 81 ASN CA CB sing N N 82 ASN CA HA sing N N 83 ASN C O doub N N 84 ASN C OXT sing N N 85 ASN CB CG sing N N 86 ASN CB HB2 sing N N 87 ASN CB HB3 sing N N 88 ASN CG OD1 doub N N 89 ASN CG ND2 sing N N 90 ASN ND2 HD21 sing N N 91 ASN ND2 HD22 sing N N 92 ASN OXT HXT sing N N 93 ASP N CA sing N N 94 ASP N H sing N N 95 ASP N H2 sing N N 96 ASP CA C sing N N 97 ASP CA CB sing N N 98 ASP CA HA sing N N 99 ASP C O doub N N 100 ASP C OXT sing N N 101 ASP CB CG sing N N 102 ASP CB HB2 sing N N 103 ASP CB HB3 sing N N 104 ASP CG OD1 doub N N 105 ASP CG OD2 sing N N 106 ASP OD2 HD2 sing N N 107 ASP OXT HXT sing N N 108 CYS N CA sing N N 109 CYS N H sing N N 110 CYS N H2 sing N N 111 CYS CA C sing N N 112 CYS CA CB sing N N 113 CYS CA HA sing N N 114 CYS C O doub N N 115 CYS C OXT sing N N 116 CYS CB SG sing N N 117 CYS CB HB2 sing N N 118 CYS CB HB3 sing N N 119 CYS SG HG sing N N 120 CYS OXT HXT sing N N 121 GLN N CA sing N N 122 GLN N H sing N N 123 GLN N H2 sing N N 124 GLN CA C sing N N 125 GLN CA CB sing N N 126 GLN CA HA sing N N 127 GLN C O doub N N 128 GLN C OXT sing N N 129 GLN CB CG sing N N 130 GLN CB HB2 sing N N 131 GLN CB HB3 sing N N 132 GLN CG CD sing N N 133 GLN CG HG2 sing N N 134 GLN CG HG3 sing N N 135 GLN CD OE1 doub N N 136 GLN CD NE2 sing N N 137 GLN NE2 HE21 sing N N 138 GLN NE2 HE22 sing N N 139 GLN OXT HXT sing N N 140 GLU N CA sing N N 141 GLU N H sing N N 142 GLU N H2 sing N N 143 GLU CA C sing N N 144 GLU CA CB sing N N 145 GLU CA HA sing N N 146 GLU C O doub N N 147 GLU C OXT sing N N 148 GLU CB CG sing N N 149 GLU CB HB2 sing N N 150 GLU CB HB3 sing N N 151 GLU CG CD sing N N 152 GLU CG HG2 sing N N 153 GLU CG HG3 sing N N 154 GLU CD OE1 doub N N 155 GLU CD OE2 sing N N 156 GLU OE2 HE2 sing N N 157 GLU OXT HXT sing N N 158 GLY N CA sing N N 159 GLY N H sing N N 160 GLY N H2 sing N N 161 GLY CA C sing N N 162 GLY CA HA2 sing N N 163 GLY CA HA3 sing N N 164 GLY C O doub N N 165 GLY C OXT sing N N 166 GLY OXT HXT sing N N 167 HIS N CA sing N N 168 HIS N H sing N N 169 HIS N H2 sing N N 170 HIS CA C sing N N 171 HIS CA CB sing N N 172 HIS CA HA sing N N 173 HIS C O doub N N 174 HIS C OXT sing N N 175 HIS CB CG sing N N 176 HIS CB HB2 sing N N 177 HIS CB HB3 sing N N 178 HIS CG ND1 sing Y N 179 HIS CG CD2 doub Y N 180 HIS ND1 CE1 doub Y N 181 HIS ND1 HD1 sing N N 182 HIS CD2 NE2 sing Y N 183 HIS CD2 HD2 sing N N 184 HIS CE1 NE2 sing Y N 185 HIS CE1 HE1 sing N N 186 HIS NE2 HE2 sing N N 187 HIS OXT HXT sing N N 188 HOH O H1 sing N N 189 HOH O H2 sing N N 190 ILE N CA sing N N 191 ILE N H sing N N 192 ILE N H2 sing N N 193 ILE CA C sing N N 194 ILE CA CB sing N N 195 ILE CA HA sing N N 196 ILE C O doub N N 197 ILE C OXT sing N N 198 ILE CB CG1 sing N N 199 ILE CB CG2 sing N N 200 ILE CB HB sing N N 201 ILE CG1 CD1 sing N N 202 ILE CG1 HG12 sing N N 203 ILE CG1 HG13 sing N N 204 ILE CG2 HG21 sing N N 205 ILE CG2 HG22 sing N N 206 ILE CG2 HG23 sing N N 207 ILE CD1 HD11 sing N N 208 ILE CD1 HD12 sing N N 209 ILE CD1 HD13 sing N N 210 ILE OXT HXT sing N N 211 LEU N CA sing N N 212 LEU N H sing N N 213 LEU N H2 sing N N 214 LEU CA C sing N N 215 LEU CA CB sing N N 216 LEU CA HA sing N N 217 LEU C O doub N N 218 LEU C OXT sing N N 219 LEU CB CG sing N N 220 LEU CB HB2 sing N N 221 LEU CB HB3 sing N N 222 LEU CG CD1 sing N N 223 LEU CG CD2 sing N N 224 LEU CG HG sing N N 225 LEU CD1 HD11 sing N N 226 LEU CD1 HD12 sing N N 227 LEU CD1 HD13 sing N N 228 LEU CD2 HD21 sing N N 229 LEU CD2 HD22 sing N N 230 LEU CD2 HD23 sing N N 231 LEU OXT HXT sing N N 232 PHE N CA sing N N 233 PHE N H sing N N 234 PHE N H2 sing N N 235 PHE CA C sing N N 236 PHE CA CB sing N N 237 PHE CA HA sing N N 238 PHE C O doub N N 239 PHE C OXT sing N N 240 PHE CB CG sing N N 241 PHE CB HB2 sing N N 242 PHE CB HB3 sing N N 243 PHE CG CD1 doub Y N 244 PHE CG CD2 sing Y N 245 PHE CD1 CE1 sing Y N 246 PHE CD1 HD1 sing N N 247 PHE CD2 CE2 doub Y N 248 PHE CD2 HD2 sing N N 249 PHE CE1 CZ doub Y N 250 PHE CE1 HE1 sing N N 251 PHE CE2 CZ sing Y N 252 PHE CE2 HE2 sing N N 253 PHE CZ HZ sing N N 254 PHE OXT HXT sing N N 255 PRO N CA sing N N 256 PRO N CD sing N N 257 PRO N H sing N N 258 PRO CA C sing N N 259 PRO CA CB sing N N 260 PRO CA HA sing N N 261 PRO C O doub N N 262 PRO C OXT sing N N 263 PRO CB CG sing N N 264 PRO CB HB2 sing N N 265 PRO CB HB3 sing N N 266 PRO CG CD sing N N 267 PRO CG HG2 sing N N 268 PRO CG HG3 sing N N 269 PRO CD HD2 sing N N 270 PRO CD HD3 sing N N 271 PRO OXT HXT sing N N 272 SER N CA sing N N 273 SER N H sing N N 274 SER N H2 sing N N 275 SER CA C sing N N 276 SER CA CB sing N N 277 SER CA HA sing N N 278 SER C O doub N N 279 SER C OXT sing N N 280 SER CB OG sing N N 281 SER CB HB2 sing N N 282 SER CB HB3 sing N N 283 SER OG HG sing N N 284 SER OXT HXT sing N N 285 THR N CA sing N N 286 THR N H sing N N 287 THR N H2 sing N N 288 THR CA C sing N N 289 THR CA CB sing N N 290 THR CA HA sing N N 291 THR C O doub N N 292 THR C OXT sing N N 293 THR CB OG1 sing N N 294 THR CB CG2 sing N N 295 THR CB HB sing N N 296 THR OG1 HG1 sing N N 297 THR CG2 HG21 sing N N 298 THR CG2 HG22 sing N N 299 THR CG2 HG23 sing N N 300 THR OXT HXT sing N N 301 TRP N CA sing N N 302 TRP N H sing N N 303 TRP N H2 sing N N 304 TRP CA C sing N N 305 TRP CA CB sing N N 306 TRP CA HA sing N N 307 TRP C O doub N N 308 TRP C OXT sing N N 309 TRP CB CG sing N N 310 TRP CB HB2 sing N N 311 TRP CB HB3 sing N N 312 TRP CG CD1 doub Y N 313 TRP CG CD2 sing Y N 314 TRP CD1 NE1 sing Y N 315 TRP CD1 HD1 sing N N 316 TRP CD2 CE2 doub Y N 317 TRP CD2 CE3 sing Y N 318 TRP NE1 CE2 sing Y N 319 TRP NE1 HE1 sing N N 320 TRP CE2 CZ2 sing Y N 321 TRP CE3 CZ3 doub Y N 322 TRP CE3 HE3 sing N N 323 TRP CZ2 CH2 doub Y N 324 TRP CZ2 HZ2 sing N N 325 TRP CZ3 CH2 sing Y N 326 TRP CZ3 HZ3 sing N N 327 TRP CH2 HH2 sing N N 328 TRP OXT HXT sing N N 329 TYR N CA sing N N 330 TYR N H sing N N 331 TYR N H2 sing N N 332 TYR CA C sing N N 333 TYR CA CB sing N N 334 TYR CA HA sing N N 335 TYR C O doub N N 336 TYR C OXT sing N N 337 TYR CB CG sing N N 338 TYR CB HB2 sing N N 339 TYR CB HB3 sing N N 340 TYR CG CD1 doub Y N 341 TYR CG CD2 sing Y N 342 TYR CD1 CE1 sing Y N 343 TYR CD1 HD1 sing N N 344 TYR CD2 CE2 doub Y N 345 TYR CD2 HD2 sing N N 346 TYR CE1 CZ doub Y N 347 TYR CE1 HE1 sing N N 348 TYR CE2 CZ sing Y N 349 TYR CE2 HE2 sing N N 350 TYR CZ OH sing N N 351 TYR OH HH sing N N 352 TYR OXT HXT sing N N 353 VAL N CA sing N N 354 VAL N H sing N N 355 VAL N H2 sing N N 356 VAL CA C sing N N 357 VAL CA CB sing N N 358 VAL CA HA sing N N 359 VAL C O doub N N 360 VAL C OXT sing N N 361 VAL CB CG1 sing N N 362 VAL CB CG2 sing N N 363 VAL CB HB sing N N 364 VAL CG1 HG11 sing N N 365 VAL CG1 HG12 sing N N 366 VAL CG1 HG13 sing N N 367 VAL CG2 HG21 sing N N 368 VAL CG2 HG22 sing N N 369 VAL CG2 HG23 sing N N 370 VAL OXT HXT sing N N 371 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1RTU _pdbx_initial_refinement_model.details 'PDB ENTRY 1RTU' # _atom_sites.entry_id 3AGO _atom_sites.fract_transf_matrix[1][1] 0.028913 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.009944 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.025365 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.033416 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C CA CL N O P S # loop_